Metabolite Profiling Experiments

The GC-MS metabolite profiling experiments given below are made
publicly available to get feedback from the community. The relative metabolite concentrations
are normalised according to fresh weight (or comparable quantitative data, such
as volume, cell count, etc.) and internal standards (e.g. ribotol). Although these
details are accessible within the GMD, they are not made available on the web site
so far. For these details please refer to the publication. As it is our intention
to increase the breadth GMD’s experiment repository in terms of organisms, organs
and stresses, we actively work on cross experiment normalisation and thus, profile
data and data representation might change in the future without any further notice.
For maximal quality assessment, all experiments are described using the XEML framework (see tree below), while the
GC-MS chromatograms are processed using the TagFinder software.

Mining for metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus (C)contact: kopka@mpimp-golm.mpg.dedescription: Mining for robust transcriptional and metabolic responses
to long-term salt stress: a case study on the model legume
Lotus japonicus.
Translational genomics, the use of model species to generate
knowledge about biological processes and the functions
of genes, offers great promise to biotechnologists. Few
studies have sought robust responses of model plants to
environmental stresses, such as salinity, by altering the
stress dosage or by repeating experiments in consecutive
years and/or different seasons.We mined our published and
unpublished data on legume salt acclimation for robust
system features at the ionomic, transcriptomic and metabolomic
levels. We analysed data from the model legume
Lotus japonicus, obtained through six independent, longterm,
non-lethal salt stress experiments which were carried
out over two consecutive years. Best possible controlled
greenhouse conditions were applied and two main questions
asked: how reproducible are results obtained from
physiologically meaningful salinity experiments, and what
degree of bias may be expected if conclusions are drawn
from less well-repeated sampling?A surprisingly large fraction
of the transcriptional and metabolic responses to salt
stress were not reproducible between experiments. A core
set of robust changes was found that was shared between
experiments. Many of these robust responses were qualitatively
and quantitatively conserved between different
accessions of the same species, indicating that the robust
responses may be a sound starting point for translational
genomics.
start date: 2006-01-01experiment Id:
cdb1fa79-b1a7-4e18-9caf-54eb2f3bb6a1links: metabolite profileMapMan pathwayXEML experimental descriptionISA-Tab exportTagList Metabolite raw exportTagList Metabolite norm exportTagList Analyte raw exportTagList Analyte norm exportTagList MST raw export

This tree schematises the experimental design
of a single metabolite profiling experiment with the x-axis representing the time
scale. Branches of the tree are used to describe the plant’s environmental condition.
Recorded environmental conditions are either given to describe the general experimental
setup and to support cross experiment comparisons, or to indicate the specific stress
type. A “salt stress experiment” is described using different salt concentrations.
Clicking the nodes of the tree, quantitative environmental conditions (e.g. temperature,
salt concentrations, humidity, etc.) describing the plant’s environment can be inspected
in the right table. Unfortunately, due to the limitations of the current html based
visualisation, the scaling of the tree's branches is not proportional to the real
length of time. Green tagged observation points (OP) represent sampling time points.
Results in the data analysis (see heat map or MapMan links in table on top) correspond
to these observation points. Please note that observation point names (OP1, OP2,
etc.) do not relate to each other. Instead, use the description of the observation
points to identify potential candidates for cross experiment profile comparison.